Diffusion Basis Function and a tractography
method for FiberCup-2009.

D.Sc. Alonso Ramirez Manzanares [alram@cimat.mx]    


Introduction:

This page contains all the data and programas that run our tractography method for the FiberCup 2009 Challenge.

In order to make the things simple we put all the data and programs in a single ZIP file (see below). This ZIP file contains everything: two toolboxes (Multi-tensor Fitting and tractography),  the Fiber Cup Diffusion Weighted MR data, and even, the nifti library for Matlab (niftimatlib-1.0) that we use all the time for read and write MR data.

You can find additional/theoretical information about this package at:

 - The Diffusion Basis Function paper.
 - The tractography article we submitted to the FiberCup 2009 Challenge.
 - The nifti library for Matlab "niftimatlib-1.0" (just in case you want check details about the library).


Downloads:

Data and Programas ZIP FILE


Installation and execution instructions:

a) Lets assume that you decompress the ZIP file in folder named /instalation_folder/
b) Add the following toolbox paths to the Matlab's path

/instalation_folder/DBF_matlab/niftimatlib-1.0/matlab/
/instalation_folder/DBF_matlab/
/instalation_folder/DBF_matlab/dbf_toolbox/
/instalation_folder/DBF_matlab/tracto_toolbox/

c) Edit in Matlab the script file /instalation_folder/DBF_matlab/main_launcher.m

Change the first line according to your system:
instalation_folder = '/instalation_folder';

d) Run the script /instalation_folder/DBF_matlab/main_launcher.m in Matlab. You should see the results in the figure below:

result

 e) The coordinates of the tractography for the 16 seed points are in the files (see the FiberCup 2009 Challenge rules):

/instalation_folder/rawData/File1.txt
...
/instalation_folder/rawData/File16.txt


Trouble Shooting Section

If you get the following error:

??? Error using ==> file2mat at 16
file2mat.c not compiled - see Makefile
it is because you have to compile the niftimatlib for your system as follows :

a) Inside Matlab console change the directory to /instalation_folder/DBF_matlab/niftimatlib-1.0/matlab/@file_array/private/src

b) Compile the following C sources with the matlab's mex compiler as follows:
>> mex file2mat.c
>> mex mat2file.c

 c) move the new files  file2mat.XX and  mat2file.XX to   /instalation_folder/DBF_matlab/niftimatlib-1.0/matlab/@file_array/private/